Scaling up to whole-genome annotation, things seem to be going well. However, there are some intermittent issues. I've seen a couple occurrences of the following error...<div><br></div><blockquote style="margin:0px 0px 0px 40px;border:none;padding:0px">
<div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div>
</div><div><div><font face="courier new, monospace">running est2genome search.</font></div></div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new, monospace">Widget::exonerate::est2genome:</font></div>
</div><div><div><font face="courier new, monospace">/N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq101.for.716125-721460.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.0.fasta -Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/scaffold_23.716125-721460.comp58983_c0_seq101.est_exonerate.0</font></div>
</div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div>
</div><div><div><font face="courier new, monospace">couldn't close /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.5.mason.maker.output/maker.pdom.5.mason_datastore/scaffold_23/theVoid.scaffold_23/comp58983_c0_seq37.for.716125-723330.0.fasta at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/FastaFile.pm line 60.</font></div>
</div><div><div><font face="courier new, monospace">--> rank=NA, hostname=c4</font></div></div><div><div><font face="courier new, monospace">ERROR: Failed while polishig ESTs</font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level:2, tier_type:2</font></div>
</div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_23</font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level:5, tier_type:0</font></div>
</div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_23</font></div></div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">examining contents of the fasta file and run log</font></div>
</div><div><div><font face="courier new, monospace">Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new, monospace">Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div>
</div><div><div><font face="courier new, monospace">Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div></blockquote><div><br></div><div><br>
</div><div>...as well as one occurrence of this error.</div><div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px"><div><div><font face="courier new, monospace">#-------------------------------#</font></div>
</div><div><div><font face="courier new, monospace">Calling out to FastaSeq::convert at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 1480.</font></div></div><div><div><font face="courier new, monospace">running est2genome search.</font></div>
</div><div><div><font face="courier new, monospace">#--------- command -------------#</font></div></div><div><div><font face="courier new, monospace">Widget::exonerate::est2genome:</font></div></div><div><div><font face="courier new, monospace">/N/hd01/dstandag/Mason/local/bin/exonerate -q /N/dc/scratch/dstandag/PdomGenomic/Annotation/output/maker.pdom.3.mason.maker.output/maker.pd</font></div>
</div><div><div><font face="courier new, monospace">om.3.mason_datastore/scaffold_7/theVoid.scaffold_7/comp59027_c1_seq93.for.1869077-1869882.0.fasta -t /N/dc/scratch/dstandag/PdomGenomic/Anno</font></div></div><div><div>
<font face="courier new, monospace">tation/output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.0.fasta </font></div></div><div><div><font face="courier new, monospace">-Q dna -T dna --model est2genome --minintron 20 --maxintron 10000 --showcigar --percent 20 > /N/dc/scratch/dstandag/PdomGenomic/Annotation/</font></div>
</div><div><div><font face="courier new, monospace">output/maker.pdom.3.mason.maker.output/maker.pdom.3.mason_datastore/scaffold_7/theVoid.scaffold_7/scaffold_7.1869077-1869882.comp59027_c1_se</font></div></div><div><div>
<font face="courier new, monospace">q93.est_exonerate.0</font></div></div><div><div><font face="courier new, monospace">#-------------------------------#</font></div></div><div><div><font face="courier new, monospace"><br>
</font></div></div><div><div><font face="courier new, monospace">------------- EXCEPTION: Bio::Root::Exception -------------</font></div></div><div><div><font face="courier new, monospace">MSG: Sequence is a protein. Cannot revcom</font></div>
</div><div><div><font face="courier new, monospace">STACK: Error::throw</font></div></div><div><div><font face="courier new, monospace">STACK: Bio::Root::Root::throw /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/Root/Root.pm:368</font></div>
</div><div><div><font face="courier new, monospace">STACK: Bio::PrimarySeqI::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/PrimarySeqI.pm:381</font></div></div><div><div><font face="courier new, monospace">STACK: Bio::LocatableSeq::revcom /N/u/dstandag/Mason/local/src/PerlLibs/lib/perl5/Bio/LocatableSeq.pm:577</font></div>
</div><div><div><font face="courier new, monospace">STACK: exonerate::splice_info::needs_to_be_revcomped /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/exonerate/<a href="http://splice_info.pm:86">splice_info.pm:86</a></font></div>
</div><div><div><font face="courier new, monospace">STACK: Widget::exonerate::est2genome::assemble /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/<a href="http://est2genome.pm:686">est2genome.pm:686</a></font></div>
</div><div><div><font face="courier new, monospace">STACK: Widget::exonerate::est2genome::parse /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Widget/exonerate/<a href="http://est2genome.pm:961">est2genome.pm:961</a></font></div>
</div><div><div><font face="courier new, monospace">STACK: polisher::exonerate::est::e_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/<a href="http://est.pm:82">est.pm:82</a></font></div>
</div><div><div><font face="courier new, monospace">STACK: polisher::exonerate::est::polish /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/polisher/exonerate/<a href="http://est.pm:44">est.pm:44</a></font></div></div>
<div><div><font face="courier new, monospace">STACK: GI::to_polisher /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1670</font></div></div><div><div><font face="courier new, monospace">STACK: GI::polish_exonerate /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm:1517</font></div>
</div><div><div><font face="courier new, monospace">STACK: Process::MpiChunk::_go /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:1663</font></div></div><div><div><font face="courier new, monospace">STACK: Process::MpiChunk::run /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:335</font></div>
</div><div><div><font face="courier new, monospace">STACK: Process::MpiChunk::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm:351</font></div></div><div><div><font face="courier new, monospace">STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286</font></div>
</div><div><div><font face="courier new, monospace">STACK: Process::MpiTiers::run_all /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiTiers.pm:286</font></div></div><div><div><font face="courier new, monospace">STACK: /N/u/dstandag/Mason/local/src/maker-dev/bin/maker:644</font></div>
</div><div><div><font face="courier new, monospace">-----------------------------------------------------------</font></div></div><div><div><font face="courier new, monospace">--> rank=NA, hostname=c4</font></div></div>
<div><div><font face="courier new, monospace">ERROR: Failed while polishig ESTs</font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level:2, tier_type:2</font></div></div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_7</font></div>
</div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">ERROR: Chunk failed at level:5, tier_type:0</font></div></div><div><div><font face="courier new, monospace">FAILED CONTIG:scaffold_7</font></div>
</div><div><div><font face="courier new, monospace"><br></font></div></div><div><div><font face="courier new, monospace">examining contents of the fasta file and run log</font></div></div><div><div><font face="courier new, monospace">Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div>
</div><div><div><font face="courier new, monospace">Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new, monospace">Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div>
</div></blockquote><div><br></div><div>I'll let you know if I see anything else.</div><div class="gmail_extra"><br clear="all"><br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>
Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br>
<br><br><div class="gmail_quote">On Wed, Nov 7, 2012 at 11:46 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Thanks. Typo now fixed on my end too ;-)</div><div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Wednesday, 7 November, 2012 11:43 AM<div>
<div class="h5"><br><span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: Maker issues<br></div></div></div><div><div class="h5"><div><br></div>Looked good for a while, but came across this error.<div><br></div><blockquote style="margin:0 0 0 40px;border:none;padding:0px">
<div><div><font face="courier new,monospace">total clusters:20 now processing 0</font></div></div><div><div><font face="courier new,monospace">flattening EST clusters</font></div></div><div><div><font face="courier new,monospace">doing tblastx of alt-ESTs</font></div>
</div><div><div><font face="courier new,monospace">Undefined subroutine &GI::loalize_file called at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/GI.pm line 2648.</font></div></div><div><div><font face="courier new,monospace">--> rank=NA, hostname=c4</font></div>
</div><div><div><font face="courier new,monospace">ERROR: Failed while doing tblastx of alt-ESTs</font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:4, tier_type:2</font></div></div>
<div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_58</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">ERROR: Chunk failed at level:5, tier_type:0</font></div>
</div><div><div><font face="courier new,monospace">FAILED CONTIG:scaffold_58</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">examining contents of the fasta file and run log</font></div>
</div><div><div><font face="courier new,monospace">Calling Datastore::MD5::mkdir at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new,monospace">Calling uri_escape at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div>
</div><div><div><font face="courier new,monospace">Calling File::Path::mkpath at /N/hd01/dstandag/Mason/local/src/maker-dev/bin/../lib/Process/MpiChunk.pm line 433.</font></div></div><div><div><font face="courier new,monospace"><br>
</font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace"><br></font></div></div><div><div><font face="courier new,monospace">--Next Contig--</font></div>
</div></blockquote><div><br></div><div>It seems pretty clear that there is a typo in GI.pm. I changed <b>loalize</b> to <b>localize</b> and relaunched.</div><div class="gmail_extra"><br clear="all"><br>--<br>Daniel S. Standage<br>
Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br><br><br><div class="gmail_quote">On Wed, Nov 7, 2012 at 9:30 AM, Daniel Standage <span dir="ltr"><<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Done.<div><br></div><div>Test job has successfully cleared the preliminary Fasta indexing steps and is repeat masking. I'll let you know if there are any problems. Thanks!</div><div class="gmail_extra"><div><br clear="all">
<br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br><br><br></div><div><div><div class="gmail_quote">
On Wed, Nov 7, 2012 at 9:00 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>1.006902 Bio::Root::Version /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live/Bio/Root/Version.pm</div><div><br></div><div>
One thing I noticed, in the debug output is that you are using Bioperl live (here --> /N/u/dstandag/Mason/local/src/PerlLibs/bioperl-live). It's fasta indexer is broken. I have an open bug I am trying to resolve with the Bioperl developers, but for now use the CPAN version of Bioperl.</div>
<div><br></div><div>Thanks,</div><div>Carson</div><div><br></div><div><br></div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 5 November, 2012 10:14 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>><br><span style="font-weight:bold">Cc: </span> Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Re: Maker issues<br></div><div><div><div><br></div>Debug output attached (bzip2 compressed).<div class="gmail_extra"><br clear="all"><br>--<br>Daniel S. Standage<br>
Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>
Iowa State University<br><br><br><br><div class="gmail_quote">On Mon, Nov 5, 2012 at 10:08 AM, Carson Holt <span dir="ltr"><<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div style="font-size:14px;font-family:Calibri,sans-serif;word-wrap:break-word"><div>Thanks. Could you also run with the --debug flag set on the command line for a few minutes and send me that.</div>
<div><br></div><div>--Carson</div><div><br></div><div><br></div><span><div style="border-right:medium none;padding-right:0in;padding-left:0in;padding-top:3pt;text-align:left;font-size:11pt;border-bottom:medium none;font-family:Calibri;border-top:#b5c4df 1pt solid;padding-bottom:0in;border-left:medium none">
<span style="font-weight:bold">From: </span> Daniel Standage <<a href="mailto:daniel.standage@gmail.com" target="_blank">daniel.standage@gmail.com</a>><br><span style="font-weight:bold">Date: </span> Monday, 5 November, 2012 10:05 AM<br>
<span style="font-weight:bold">To: </span> Carson Holt <<a href="mailto:carsonhh@gmail.com" target="_blank">carsonhh@gmail.com</a>>, Maker Mailing List <<a href="mailto:maker-devel@yandell-lab.org" target="_blank">maker-devel@yandell-lab.org</a>><br>
<span style="font-weight:bold">Subject: </span> Maker issues<br></div><div><div><div><br></div>Carson,<div><br></div><div>I updated to the latest development version, made sure the TMP directory is on native disk space, and relaunched. I have attached the output of the job that failed in <5 minutes. It looks pretty similar to the errors I got the last time I used the dev version.<br clear="all">
<br>--<br>Daniel S. Standage<br>Ph.D. Candidate<br>Bioinformatics and Computational Biology Program<br>Department of Genetics, Development, and Cell Biology<br>Iowa State University<br><br></div></div></div></span></div>
</blockquote>
</div><br></div></div></div></span></div></blockquote></div><br></div></div></div></blockquote></div><br></div></div></div></span></div>
</blockquote></div><br></div>